Recent developments in DNA sequencing technology now enable sequencing of the human genome for less than US$1,000 making whole genome sequencing affordable for routine diagnostics for increasingly larger sets of cancer patients. Hundreds of thousands of patient genomes will become sequenced in the next few years, and in Germany alone we expect completion of >25,000 individual cancer genomes by 2018. While those estimates are made on the basis that for each tumor only one sample is sequenced it has become clear that averaging over millions of cells in a given tumor sample may hide subtle, but clinically important genomic alterations that are only present in a small fraction of cells. Here, I will report on our recent development of an integrated imaging and sequencing pipeline that allows growing of microtissues from single patient derived cancer cells, dynamic phenotyping of those microtissues over many days and subsequent harvesting of individual cells followed by molecular sequencing. By this strategy, we aim to integrate sequencing with image-based phenotyping and drug profiling ex vivo of patient derived single cancer cells to comprehensively tackle intratumour cellular heterogeneity.